[gmx-users] oplsaa parametrization

[R. A.]

Dear Users
I m trying to simulate a structure (not a protein) which is not
parametrized in oplsaa FF. I created the structure using PRODRG and
included the results of *.itp from PRODRG to ffoplsaa.rtp file and tried
to use available oplss_xxx for my atom type near to those ones already
exists in *.atp. I also optimized my structure at RHF/6-31G* level and
calculated the charge using resp. Then updated ffoplsaa.rtp using this
calculated charge. By refering to the mailing list it seems that I need
to modify bn.itp and nob.itp file as well (?!). I m just wonder if
anybody use PRODRG how he/she parametrized FF. As I m new in GROMACS and
any tutorial or procedure to follow will help me so much. Thank you in
advance for any ideas or comments.

Also when I use pdb2gmx, I have this warning; all CONECT records are
ignored. However when I proceed with energy minization in vacuum the
program doesnt complain and it can produce *.tpr file.

Regards
Rosa

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